The game against Tividale at home on November 5 last year saw Alport 3-0 up t half time when their opponents refused to play on after the break due to an alleged racist incident.
Whitchurch were asked by both The FA and Midland Football League, to submit match observations and took witness statements from people who were present at the game.
The club was told by the Staffordshire FA last month that the matter was not being pursued further and the investigation was closed.
The league have now awarded the three points to Alport, with no goals credited to either team.
After the ruling, Whitchurch issued a statement which read: "Whitchurch Alport FC welcomes the decisions from The FA and Midland Football League and would like to thank all who assisted the club during the investigation.
"The club would like to reiterate that it does not tolerate abuse of any nature and we will continue to work hard to ensure that our ground is a safe and welcoming environment for all supporters, staff and players.
"The club now deems this incident closed and no further statements will be made."